My question is two people with same gotra can marry?
If can't then what is the reason behind it.

In Hindu society marrying within the same gotra is equivalent to incest. "Gotra" is a term used for lineage - being in the same gotra means sharing a common male ancestor. However, once a woman marries her gotra becomes the same as her husband's. As a consequence it's actually possible for first cousins to wed - for example if a brother has a son, and his sister marries someone in a different gotra and then has a daughter, that son and daughter are considered to be of different gotras and could wed.

Interesting.

I assume the OP is in India and is asking about Indian law.

I think the following (https://en.wikipedia.org/wiki/Gotra) may be pertinent:

"Legal situation[edit (https://en.wikipedia.org/w/index.php?title=Gotra&action=edit&section=4)]Khap panchayats in Haryana have been making a huge fuss over banning "same gotra marriages." Kadyan Khap International convener Naresh Kadyan had moved a petition seeking amendment to the Hindu Marriage Act (HMA) to legally prohibit marriages in the same gotra. However, the petition was dismissed as withdrawn after a vacation. Bench of Justices S N Dhingra and A K Pathak of the Delhi High Court warned that a heavy cost would be imposed on the petitioner for wasting the time of the court.
In course of the proceedings, the bench observed,

“You don’t know what is a gotra. Which Hindu text prescribes banning of sagotra (same clan) marriage? Why are you wasting the time of the court? If you are not able to substantiate your words, then you should not have come before the court.”[8] (https://en.wikipedia.org/wiki/Gotra#cite_note-8)
In the court case "Madhavrao vs Raghavendrarao" which involved a Deshastha Brahmin couple, the German scholar Max Mueller's definition of gotra as descending from eight sages and then branching out to several families was thrown out by reputed judges of a Bombay High Court.[9] (https://en.wikipedia.org/wiki/Gotra#cite_note-9) The court called the idea of Brahmin families descending from an unbroken line of common ancestors as indicated by the names of their respective gotras "impossible to accept."[10] (https://en.wikipedia.org/wiki/Gotra#cite_note-10) The court consulted relevant Hindu texts and stressed the need for Hindu society and law to keep up with the times, emphasizing that notions of good social behavior and the general ideology of the Hindu society had changed.[11] (https://en.wikipedia.org/wiki/Gotra#cite_note-11) The court also said that the mass of material in the Hindu texts is so vast and full of contradictions that it is almost an impossible task to reduce it to order and coherence."

My question is
If I want to marry one girl and her sister got married with a person whoose gotra is similar to my Fraternal aunt's gotra. Here my confusion what would be the relation between me and her sister.Is it Brother and Sister. Is this is correct.can any one explain.

If the Delhi High Court can't figure it out, how do you expect us to do so? :)

I suggest you ask a lawyer in your country. And ask in particular if it is a matter of law, or merely of religious custom.